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Yorodumi- PDB-2ipk: Crystal Structure of the MHC Class II Molecule HLA-DR1 in Complex... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2ipk | ||||||
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Title | Crystal Structure of the MHC Class II Molecule HLA-DR1 in Complex with the Fluorogenic Peptide, AcPKXVKQNTLKLAT (X=3-[5-(dimethylamino)-1,3-dioxo-1,3-dihydro-2H-isoindol-2-yl]-L-alanine) and the Superantigen, SEC3 Variant 3B2 | ||||||
Components |
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Keywords | IMMUNE SYSTEM / HLA / DR1 / MHC / Major Histocompatibility Complex / Fluorogenic Probe / SEC3 / 4-(N / N-dimethylamino)phthalimidoalanyl / DAPA | ||||||
Function / homology | Function and homology information regulation of interleukin-4 production / regulation of interleukin-10 production / positive regulation of T cell mediated immune response to tumor cell / myeloid dendritic cell antigen processing and presentation / antigen processing and presentation of endogenous peptide antigen via MHC class II / autolysosome membrane / regulation of T-helper cell differentiation / positive regulation of CD4-positive, CD25-positive, alpha-beta regulatory T cell differentiation / MHC class II receptor activity / positive regulation of CD4-positive, alpha-beta T cell activation ...regulation of interleukin-4 production / regulation of interleukin-10 production / positive regulation of T cell mediated immune response to tumor cell / myeloid dendritic cell antigen processing and presentation / antigen processing and presentation of endogenous peptide antigen via MHC class II / autolysosome membrane / regulation of T-helper cell differentiation / positive regulation of CD4-positive, CD25-positive, alpha-beta regulatory T cell differentiation / MHC class II receptor activity / positive regulation of CD4-positive, alpha-beta T cell activation / antigen processing and presentation of peptide or polysaccharide antigen via MHC class II / positive regulation of memory T cell differentiation / positive regulation of monocyte differentiation / CD4 receptor binding / inflammatory response to antigenic stimulus / positive regulation of kinase activity / intermediate filament / transport vesicle membrane / T-helper 1 type immune response / polysaccharide binding / Translocation of ZAP-70 to Immunological synapse / Phosphorylation of CD3 and TCR zeta chains / positive regulation of insulin secretion involved in cellular response to glucose stimulus / humoral immune response / macrophage differentiation / negative regulation of type II interferon production / Generation of second messenger molecules / immunological synapse / PD-1 signaling / negative regulation of T cell proliferation / epidermis development / detection of bacterium / negative regulation of inflammatory response to antigenic stimulus / MHC class II antigen presentation / T cell receptor binding / trans-Golgi network membrane / lumenal side of endoplasmic reticulum membrane / protein tetramerization / clathrin-coated endocytic vesicle membrane / ER to Golgi transport vesicle membrane / cognition / structural constituent of cytoskeleton / positive regulation of T cell mediated cytotoxicity / peptide antigen assembly with MHC class II protein complex / MHC class II protein complex / peptide antigen binding / endocytic vesicle membrane / antigen processing and presentation of exogenous peptide antigen via MHC class II / positive regulation of immune response / Interferon gamma signaling / positive regulation of T cell activation / Downstream TCR signaling / MHC class II protein complex binding / late endosome membrane / T cell receptor signaling pathway / toxin activity / early endosome membrane / clathrin-dependent endocytosis of virus by host cell / positive regulation of canonical NF-kappaB signal transduction / adaptive immune response / positive regulation of MAPK cascade / positive regulation of viral entry into host cell / lysosome / positive regulation of ERK1 and ERK2 cascade / host cell surface receptor binding / immune response / apical plasma membrane / positive regulation of protein phosphorylation / lysosomal membrane / fusion of virus membrane with host plasma membrane / external side of plasma membrane / Golgi membrane / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / host cell plasma membrane / positive regulation of DNA-templated transcription / cell surface / signal transduction / extracellular space / extracellular exosome / extracellular region / membrane / metal ion binding / plasma membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) Staphylococcus aureus subsp. aureus Mu50 (bacteria) Influenza A virus | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | Nguyen, T.T. / Stern, L.J. | ||||||
Citation | Journal: Nat.Chem.Biol. / Year: 2007 Title: Fluorogenic probes for monitoring peptide binding to class II MHC proteins in living cells. Authors: Venkatraman, P. / Nguyen, T.T. / Sainlos, M. / Bilsel, O. / Chitta, S. / Imperiali, B. / Stern, L.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2ipk.cif.gz | 150.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2ipk.ent.gz | 116.6 KB | Display | PDB format |
PDBx/mmJSON format | 2ipk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ip/2ipk ftp://data.pdbj.org/pub/pdb/validation_reports/ip/2ipk | HTTPS FTP |
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-Related structure data
Related structure data | 1pywS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 21287.102 Da / Num. of mol.: 1 / Fragment: Extracellular domain, residues 26-207 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-DRA / Plasmid: pLM1 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): Bl21(de3) / References: UniProt: P01903 |
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#2: Protein | Mass: 22080.664 Da / Num. of mol.: 1 / Fragment: Extracellular domain, residues 30-219 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-DRB1 / Plasmid: pLM1 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): Bl21(de3) / References: UniProt: P04229, UniProt: P01911*PLUS |
#3: Protein/peptide | Mass: 1628.931 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: synthesized peptide / Source: (synth.) Influenza A virus / References: UniProt: A8CDU0*PLUS |
#4: Protein | Mass: 27852.264 Da / Num. of mol.: 1 / Fragment: Residues 28-266 / Mutation: K70S, L72F, A73K, H74W Source method: isolated from a genetically manipulated source Source: (gene. exp.) Staphylococcus aureus subsp. aureus Mu50 (bacteria) Species: Staphylococcus aureus / Strain: MU50/ATCC 700699 / Gene: entC3 / Production host: Escherichia coli (E. coli) / Strain (production host): Hb 2151 / References: UniProt: P0A0L3, UniProt: P0A0L5*PLUS |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 4.73 Å3/Da / Density % sol: 74 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.3 Details: PEG 4000, Ethylene Glycol, Sodium Acetate, pH 5.3, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 95 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.1 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 18, 2006 / Details: mirrors |
Radiation | Monochromator: Pt-coated toroidal Si mirror for horizontal and vertical focussing followed by double flat Si crystal monochromator Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→33 Å / Num. all: 67968 / Num. obs: 67968 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.6 % / Biso Wilson estimate: 41.3 Å2 / Rmerge(I) obs: 0.091 / Rsym value: 0.087 / Net I/σ(I): 14 |
Reflection shell | Resolution: 2.3→2.38 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.368 / Mean I/σ(I) obs: 2 / Num. unique all: 25071 / Rsym value: 0.363 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1PYW. Model of HLA-DR1 with SEC3-3b2 omitting the peptide (chain C). Resolution: 2.3→32.5 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0
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Solvent computation | Bsol: 44.506 Å2 | ||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 48.611 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.3→32.5 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.3→2.44 Å / Rfactor Rfree error: 0.014
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Xplor file |
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